Bowtie 2: bowtie build does not create .rev index files

Question

[dzisis1986]

I am trying to run bowtie-build in Bowtie2 in order to create the index files for mapping and everytime i am running my script there is a warning

Warning: Encountered reference sequence with only gaps

Furthermore when check the index files i have only *1.bt2 *2.bt2 *3.bt2 *4.bt2 files but not the .rev files and without this its not possible to use bowtie align . Here is my script for bowtie-build :

./bowtie2-build --offrate 1 AGPv4.fa  AGPv4

Any way to solve this problem ??

[Devon Ryan]

The error suggests that you have a contig with only N. Perhaps that's related to the problem.

[Fabio Marroni]

I agree with Devon. It is possible that you have one (or more) contigs with only N.

[dzisis1986]

I use as reference genome the masked version of zea mays Zea_mays.AGPv4.dna_rm.toplevel.fa . What do you suggest me to do ?

[Devon Ryan]

Never use a hard-masked fasta file. Here is an appropriate fasta file.

[dzisis1986]

Thank you i will try to use this version and see the result !

[dzisis1986]

Well, i tried to use the correct version of fasta reference as you proposed. There is no error in bowtie-build but still there are only *1.bt2 *2.bt2 *3.bt2 *4.bt2 files and again no .rev files !!!! what can be done ??

[Devon Ryan]

bowtie2-build Zea_mays.AGPv4.dna.toplevel.fa AGPv4 works for me.

[Fabio Marroni]

Try to find out if there are contigs fully composed of Ns, and if so, just remove them, since they are useless. Also, if this is the case, you might notify to the curators of the genome!

[Medhat]

which version of bowtie2 you have?

[dzisis1986]

bowtie2 2.2.4 and i cant update because i am working in a cluster

[Devon Ryan]

You never need to be root to update software, just download the binary and use it rather than what's provided on the cluster.

Answer 1

[dzisis1986]

Well, i tried to use the correct version of fasta reference as you proposed. There is no error in bowtie-build but still there are only *1.bt2 *2.bt2 *3.bt2 *4.bt2 files and again no .rev files !!!! Any idea what can be done ??